PATJ

protein-coding

PATJ crumbs cell polarity complex component, the group of MicroRNA protein coding host genes|Crumbs complex|PDZ domain containing

Gene summary

This gene encodes a protein with multiple PDZ domains. PDZ domains mediate protein-protein interactions, and proteins with multiple PDZ domains often organize multimeric complexes at the plasma membrane. This protein localizes to tight junctions and to the apical membrane of epithelial cells. A similar protein in Drosophila is a scaffolding protein which tethers several members of a multimeric signaling complex in photoreceptors. [provided by RefSeq, Jul 2008]

Previous symbols:

INADL

MANE transcript

NM_001350145.3

Inheritance

—

ClinVar variants

U:58B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr1:61,742,477-62,178,675

External References & Databases

Ensembl (ENSG00000132849)

Transcript & Mutation Effects

hg38 • Region Span ~436.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PATJ variants in ClinVar

2 Conditions Cataloged

not providedTotal: 19

not specifiedTotal: 17

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001350145.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	3 clinvar	4 clinvar	11
missense			36 clinvar	2 clinvar	3 clinvar	41
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			16 clinvar			16
Total	0	0	58	5	7	70

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001350145.3	RefSeq	NP_001337074.2	43	MANE Select
ENST00000642238.2	Ensembl	ENSP00000494277.1	43	MANE Select
NM_176877.5	RefSeq	NP_795352.3	42	Standard
ENST00000307297.8	Ensembl	ENSP00000307496.8	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Tight junction - Homo sapiens (human)
Hippo signaling pathway - Homo sapiens (human)
Human papillomavirus infection - Homo sapiens (human)
Tight junction interactions
Cell-cell junction organization

Biological Process

intracellular signal transduction
bicellular tight junction assembly

Molecular Function

protein binding

Cellular Component

centrosome
microtubule organizing center
cytosol
plasma membrane
bicellular tight junction

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371158
Coding exons: 42
Length: 421444
Individuals with no LoFs: 125236
Homozygous LoFs: 0
Heterozygous LoFs: 511
Defined: 125747
p: 0.00203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.25	854	963	0.887	0.0000500	11711
Missense (PolyPhen)		338	381.83	0.8852		4581
Synonymous	1.02	336	361	0.932	0.0000203	3530
Loss of Function	1.19	84	96.6	0.870	0.00000519	1173

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0012	notable
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.0015	0.0015	notable
East Asian	0.0048	0.0047	notable
Finnish	0.0045	0.0045	notable
European (Non-Finnish)	0.0016	0.0016	notable
South Asian	0.0019	0.0019	notable
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Scaffolding protein that may bring different proteins into adjacent positions at the cell membrane. May regulate protein targeting, cell polarity and integrity of tight junctions. May regulate the surface expression and/or function of ASIC3 in sensory neurons. May recruit ARHGEF18 to apical cell-cell boundaries (PubMed:22006950). {ECO:0000269|PubMed:11927608, ECO:0000269|PubMed:22006950}.;

Intolerance Scores

RVIS EVS: 2.27
RVIS percentile EVS: 98.24

Essentials

Essential (gene trap): N